Having Problems with stubborn pixels in GIMP.

[Non Nomen]

My suspicion is that either the layer's pixels are locked or that it's alpha channel is locked.
In the layer tab, with that layer selected, look at the frame at the top of the layer list. There are two small icons to the right of the word 'Lock:'. The brush one locks the pixels for that layer and the painting tools won't do anything (brushes, fill, etc). The other box locks the alpha channel - you can change colors but can't change the opacity. Each icon will have a little black border around it when it is active. Make sure that both of them are inactive (no solid lines around them).
[The icons reflect the status of the currently selected layer.]

So I managed to figure out what the problem was. It seems that your original suspicions about the pixels being only partially selected were correct, although I'm not sure why it was working that way as I had been using a selection from path when that happened as I remember. I only realized what the actual issue was when I started trying to work on another section, and ended up changing pixels in areas completely outside of my actual selection area which I solved by de-selecting them with the free select tool.